Struct FmIndex 

pub struct FmIndex { /* private fields */ }

An FM-index over a byte string: BWT, C array, and Occ rank table, with the suffix array retained for locate.

Build with FmIndex::new. The index supports exact-occurrence FmIndex::count, position FmIndex::locate, and full text recovery via FmIndex::inverse_bwt (the BWT round-trips).

Examples

use oxicuda_seq::string::FmIndex;

let fm = FmIndex::new(b"banana").expect("non-empty");
assert_eq!(fm.count(b"ana"), 2);
assert_eq!(fm.locate(b"ana"), vec![1, 3]);
assert_eq!(fm.count(b"xyz"), 0);
assert_eq!(fm.inverse_bwt(), b"banana");

Implementations

impl FmIndex

pub fn new(s: &[u8]) -> SeqResult<Self>

Build the FM-index of s.

Internally appends a unique sentinel, derives the BWT from the reused SA-IS suffix array, and precomputes the C and Occ tables.

Errors

Returns SeqError::EmptyInput for an empty s, consistent with the sibling string modules.

pub fn text_len(&self) -> usize

Length of the original text (excluding the sentinel).

pub fn bwt_bytes(&self, sentinel_byte: u8) -> Vec<u8>

Borrow the BWT as raw bytes, mapping the sentinel to sentinel_byte.

The sentinel has no byte value of its own, so the caller supplies the placeholder used to render it. The placeholder is not required to be absent from the text; it is purely cosmetic for inspection/printing.

pub fn inverse_bwt(&self) -> Vec<u8>

Recover the original text by inverting the BWT through the LF-mapping.

Starts at the sentinel row (row 0, since the sentinel sorts first) and walks LF backwards, emitting characters right-to-left.

pub fn count(&self, pattern: &[u8]) -> usize

Number of occurrences of pattern in the text (backward search).

Returns 0 for an empty pattern or when the pattern does not occur.

pub fn locate(&self, pattern: &[u8]) -> Vec<usize>

Sorted text positions of every occurrence of pattern.

Each row in the final backward-search range maps to a text position through the stored suffix array. Returns an empty vector for an empty or absent pattern.

Trait Implementations

impl Clone for FmIndex

fn clone(&self) -> FmIndex

Returns a duplicate of the value.

fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source.

impl Debug for FmIndex

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.